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Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these pow

Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these powerpoint slides. Executive Summary. Entered RNA transcription 6 times (6 trials) 3 times because of software problems Never entered it correctly or completely

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Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these pow

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  1. Cathy Codonon RNA Transcription(as witnessed by Yolanda Gil)NOTE: There are comments in the notes view of these powerpoint slides

  2. Executive Summary • Entered RNA transcription 6 times (6 trials) • 3 times because of software problems • Never entered it correctly or completely • No Transcription subevent in 6 trials, added when YG hand-generated KANAL’s output • In trial 1 subject decided not to follow guidelines in training material • Trial 6 is the most representative (slides 36-55)

  3. Trial 1:“Transcription”

  4. Defined top-level node “Transcription “ as a kind of Transcribe (I think) • Brings in DNA and RNA-polym • Clicks on Transcription, gets arrow “direct-object-of-change” (YG: is this a bug?) • Brings in Promoter • Tries to unify Promoter with DNA • Reads the handout with components

  5. Collapses all roles of Transcription • Draws arrow between Transcription and RNA Polymerase; calls it subevent • Brings in Terminator • Goes back to RNA Transcription text description

  6. Screenshot Direct-object- of-change subevent Transcription RNA Polymerase DNA Terminator Promoter Make Contact Break Contact Move

  7. Subevent arrow is hidden behind Screenshot instrument Transcription RNA Polymerase Direct-object- of-change DNA Terminator RNA Promoter Make Contact Break Contact Move

  8. Subevent arrow is hidden behind Screenshot instrument Transcription RNA Polymerase Direct-object- of-change DNA subevent Terminator&Action RNA Promoter&Action Make Contact Break Contact Move

  9. Subevent arrow is hidden behind Specifies Participants in Make Contact instrument Transcription RNA Polymerase Direct-object- of-change DNA subevent Terminator&Action Things Making contact RNA Promoter&Action Move Make Contact Break Contact Leaves location empty location

  10. Subevent arrow is hidden behind Specifies Participants in Break Contact instrument Transcription RNA Polymerase Direct-object- of-change Terminator&Action DNA subevent Promoter&Action RNA Things breaking contact Move Make Contact Break Contact Leaves location empty location

  11. Saves it, keeps editing • Collapses everything, uncollapses • Reorganizes things

  12. 11:40: Collapses everything, uncollapses, reorganizes Transcription subevent Direct-object- of-change DNA Move RNA Break Contact RNA Polymerase Terminator&Action Promoter&Action Make Contact

  13. We stopped for 10min • User admits to NOT have followed the steps we had specified earlier, on purpose. User just thought about all the processes and all the objects, then connected them. User prefers to do things that way. • When using the tool, user feels as if doing a puzzle and not the transcription process held in mind

  14. Notices Promoter&Action • User says it’s an error, it should not be there, user just wants the label to read Promoter • User is happy that it is a subevent, as stated: “Because the promoter is doing things”

  15. 11:57 Transcription instrument Direct-object- of-change DNA RNA & RNA Polymerase RNA Polymerase User wonders what it is and where it came from; I said “(user) dragged it”; user says “didn’t mean to”

  16. Trial 2:“Transcription-1”

  17. User waits for me for 15 min, during that time user browses through the training material • Underlines verbs in the text • Defines Transcription-1 as a kind of action • Brings in RNA, DNA, Promoter, Term, RNA-Polym • Brings in Make-contact, Move, and Break-contact

  18. Screenshot Direct-object- of-change instrument Transcription-1 RNA Polymerase DNA Terminator RNA subevent Promoter Make Contact Break Contact Move

  19. Make-contact disappears (bug) • Saved • Edited • Everything not connected to Transcription-1 disappeared • Abort trial because of software problems 

  20. Trial 3:“Transcription-2”

  21. Define transcription as action, bring in all relevant components (steps 3,4,5 of previous trial)

  22. Transcription-2 DNA I notice that Make Contact and Transcription are now unified (user probably does not know), So Transcription-2 has all the roles of Make-contact Wanted to define DNA as the object of Transcription, Drew the arrow wrong, so “object” was not in menu. I explain why

  23. Make-contact and transcription-2 were somehow unified, thus the roles Transcription The objects Making contact DNA subevent Terminator&Action RNA Promoter&Action RNA Polymerase Break Contact Move

  24. User clicks to simplify • System freezes • Abort trial because of software problems  • User makes comment about liking to collapse things and simplify; only likes to see the detail at times, “I don’t need it, but I like to see it”

  25. Trial 4:“Transcription-3”

  26. Define transcription as action, bring in all relevant components (steps 3,4,5 of previous trial) • User makes Move a subevent of Transcription-3 • User collapses Transcription-3, Move is lost and cannot get it back • Abort trial • I explain again arrows in detail

  27. Trial 5:“Transcription-4”

  28. Define transcription as action, bring in all relevant components (steps 3,4,5 of previous trial)

  29. Transcription RNA Polymerase DNA RNA subevent Terminator&Action Move seems to always end up at the left hand side (I.e., coming first) Promoter&Action Make Contact Break Contact Move

  30. Direct-object- of-change instrument Transcription RNA Polymerase DNA RNA subevent Terminator&Action Promoter&Action Make Contact Break Contact Move

  31. Direct-object- of-change instrument Transcription RNA Polymerase DNA RNA subevent Terminator&Action Promoter&Action Thing moved Make Contact Break Contact Move

  32. Subject collapses Move to get rid of detail • For each subevent (Make-Contact, Break-Contact) assigns roles and then collapses • goes too fast to take notes • Looks at the screen, says “Shall I test it?” • The screen is as in next slide:

  33. Cmap* instrument All the participants in the subevents are specified Transcription RNA Polymerase Direct-object- of-change DNA subevent RNA Move Make Contact Break Contact Terminator&Action Promoter&Action

  34. Instead of asking questions, subject decides to check knowledge by uncollapsing nodes • Move –the thing moved-> RNA polimerase • Make-contact –the things mkg ctc-> DNA and RNA polym • Break-contact –the things brkg ctc-> DNA and RNA-polym • Says actually DNA and RNA break contact, • Since there is no delete fn in software, wants to abort and make another one where Move has RNA and DNA as objects ”because RNA moves away, actually” • Says another mistake in Break-contact, should say RNA and DNA

  35. Decides to ask some questions before discarding this • Asks two questions really fast (I cannot see) • Says very confident “I know everything I did is right, because the picture was the answer”

  36. Trial 6:“Transcription-5”NOTE: Organized in “episodes”. In newer versions of powerpoint, you can see the bullets numbered (statements made by user, YG, or comments)

  37. Define Overall Process Define Transcription-5 as action, bring in all relevant components (steps 3,4,5 of Trial 2): • Defines Transcription-5 as a kind of action • Brings in RNA, DNA, Promoter, Term, RNA-Polym • Brings in Make-contact, Move, and Break-contact

  38. User specifies participants in substeps • Move- the thing moved: RNA • User says “wait, RNA polym moves” • YG says it is ok to add two moves • User says ok but didn’t do that (user forgot?) • Collapses everything and then expands • Has the same thing as in Trial 5, but has no participants specified for Make-contact and Break-Contact (see next slide)

  39. Screenshot instrument Transcription-5 RNA Polymerase Direct-object- of-change DNA subevent RNA Move Make Contact Break Contact Terminator&Action Promoter&Action

  40. User is Ready to Test Knowledge • User saves and wants to ask questions • User re-reads text description of RNA Transcription before asking questions to SHAKEN

  41. Ask Questions • What is the instrument of Transcription-5? Ans: RNA-polymerase : User says it is correct • During Tr-5, what role does the polymerase play? User notes it is an important question Ans: In Tr-5, RNA poly plays the role: BUG: nothing shown! • User tries the last item (to ask questions through cmaps) - BUG: doesn’t seem to work.

  42. Ask Questions (cont) • How many instruments are in Tr-5? Ans: only 1 (yg note:system does not say which one) • How may objects are in Tr-5? Ans: 2 • Which objects are in Tr-5? Ans:RNA and DNA User says that’s correct • User says what is the point of asking questions, it is the same as the graph. YG explains

  43. User Wants to Continue Asking • User says there is a lot of details that she would normally teach • User says she/he is done with the scenario and she wants to continue asking more questions

  44. Ask Questions (cont) • Explain Tr-5? • Ans: object: … instrument: … Subevents: Move, Make-Contact, Break-Contact, Promoter, Terminator User reads this and finds it perfectly normal!! • She wants to bring back Transcription-1 and ask questions about it. • YG suggests to stick with Tr-5 BUG: It does not say Promoter & Action Terminator & Action as it did in the cmap

  45. Running KANAL (YG notes the interface rendering is unclear) • Summary of alternative paths in simulation • Move • Step Move: • Checking Precondition: object musn’t be restrained – succeed • Warning: no effect was produced • Step Make-Contact • Checking Preconditions: the location of O1 must be the location of Make Contact – Failed Click here for suggestions • Checking Preconditions: the location of O2 must be the location of Make-Contact– Failed

  46. User Says It is Done! • YG notes the simulation is not giving useful output because of a software problem • User says the scenario is done • YG says some things not working in software, but she will simulate what the system would say if it was working ok

  47. Hand-Generated KANAL-Style Output is Presented to User • YG shows: Move • Conditions: RNA is unrestrained – Succeed • Effect: no effect! ERROR suggested fix: specify destination of RNA User says “cytoplasm” • User goes to editor, adds: RNA location place Here is where the user wants to say cytoplasm!!

  48. User confused about Fluents • User brings in Cell • User says“this is interesting, the system is asking me to edit to add more details” • Tries to connect RNA to Cell in order to say that RNA moves to Cell (i.e., cell is the destination of Move) RNA location Cell BUG: it says Place & Cell

  49. Move object RNA Polymerase Adding another Move • User Adds another Move for RNA polym • Bug: the two moves got disconnected somehow: • YG said to pretend this: Transcription subevent Move Move

  50. Hand-Generated KANAL-Style Output is Presented to User • Move • Conditions: RNA is unrestrained – Succeed • Effect: RNA is in cytoplasm • YG decides to move to another error at this point: since locations are messed up, and since the RNA has not been created anyway • YG decides to see if user realizes Transcribe substep is missing, i.e., there are no substeps to create the RNA

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